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<h1>Chromatogram builder</h1>

<h2>Description</h2>

<p>
The ADAP Chromatogram builder takes mass lists generated for each MS scan (see Mass detection) and builds a chromatogram for each mass that can be detected continuously over the scans.
Later, these chromatograms may be deconvoluted into individual peaks by the Deconvolution module.
</p>

<p>
ADAP chromatogram construction works from the largest intensity data point in the entire data file down
to the smallest.  The reasoning is that it is beneficial to begin EICs with
larger intensity data points since their m/z values tend to be more accurate. The chromatogram building steps are as follows:
</p>

We define &epsilon; to be the mass tolerance parameter m/z.
<ol>
	<li> Take all the data points in a data file, sort them by their intensities,
	and remove those points (mostly noise) below a certain intensity threshold.</li>

	<li> Starting with the most intense data point, the first EIC is created.</li>

	<li> For this EIC, establish an immutable m/z range that is the data point's
		m/z plus or minus &epsilon; where &epsilon; is specified by the user. </li>

	<li> The next data point, which will be the next most intense, is added to an
	existing EIC if its m/z value falls within its m/z range.</li>

	<li> If the next data point does not fall within an EICs m/z range, a new EIC is
	created. New EICs are only created if the point meets the minimum start intensity
	requirement set by the user. </li>

	<li> An m/z range for a new EIC is created the same way as in step (3) except the boundaries
	will be adjusted to avoid overlapping with pre-existing EICs. As an example consider an
	existing EIC with m/z range (100.000,100.020) for &epsilon;=0.01. If the new EIC is
	initialized with a data point having an m/z value of 100.025, then this new EIC will
	have a m/z range set to be (100.020,100.035) rather than (100.015, 100.035).</li>

	<li> Repeat steps (4)-(6) until all the data has been processed.</li>

	<li>Finally, a post processing step is implemented. Only EICs with a user defined number of continuous points above a user defined intensity threshold
		are kept.</li>

</ol>

<h4>Method parameters</h4>
<dl>

<dt>Mass list name</dt>
<dd>Choose a name of the mass lists to be used for building chromatograms. The mass lists must be previously generated for each MS scan by the Mass detector module.</dd>

<dt>Min group size in number of scans</dt>
<dd>In the entire chromatogram there must be at least this number of sequential scans having points above the\textit{Intensity thresh 2} set by the user.</dd>

<dt>Group intensity threshold</dt>
<dd>See above</dd>

<dt> Min highest intensity</dt>
<dd>There must be at least one point in the chromatogram that has an intensity greater than or equal to this value.</dd>


<dt>m/z tolerance</dt>
<dd>Maximum m/z difference of data points in consecutive scans in order to be connected to the same chromatogram.</dd> 

<dt>Suffix</dt>
<dd>The resulting chromatogram will be named <i>file name + suffix</i></dd> 

</dl>

<p>
The resulting chromatograms can be opened in the peak list table visualizer using a double-click:<br>
<img src="chromatograms.png" border="1">
</p>

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